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Author |
Sommeria-Klein, G.; Zinger, L.; Coissac, E.; Iribar, A.; Schimann, H.; Taberlet, P.; Chave, J. |
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Title |
Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest |
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Journal Article |
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Year |
2020 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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Volume |
20 |
Issue |
2 |
Pages |
371-386 |
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Keywords |
community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology |
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Abstract |
High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd |
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Laboratoire d’Ecologie des Forêts de Guyane (EcoFoG, UMR 745), INRA, AgroParisTech, CIRAD, CNRS, University of the French West Indies, University of French Guiana, Kourou, France |
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Blackwell Publishing Ltd |
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1755098x (Issn) |
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EcoFoG @ webmaster @ |
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981 |
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Birer, C.; Tysklind, N.; Zinger, L.; Duplais, C. |
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Title |
Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria |
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Journal Article |
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Year |
2017 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol Ecol Resour |
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Volume |
17 |
Issue |
6 |
Pages |
e34-e45 |
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Keywords |
16S rRNA; bacterial communities; cuticular microbiome; insect cuticle; metabarcoding |
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High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment. |
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1755-0998 |
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EcoFoG @ webmaster @ |
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781 |
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Perrot, T.; Guillaume, S.; Nadine, A.; Jacques, B.; Philippe, G.; Stéphane, D.; Rodnay, S.; Mélanie, M.-R.; Eric, G. |
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Title |
A reverse chemical ecology approach to explore wood natural durability |
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Journal Article |
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Year |
2020 |
Publication |
Microbial Biotechnology |
Abbreviated Journal |
Microb. Biotechnol. |
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13 |
Issue |
5 |
Pages |
1673-1677 |
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Keywords |
glutathione transferase; Article; biodegradation; data base; detoxification; ecology; enzyme activity; enzyme metabolism; forest; molecular dynamics; physical parameters; species identification; thermal analysis; Trametes versicolor; wood; wood durability |
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The natural durability of wood species, defined as their inherent resistance to wood-destroying agents, is a complex phenomenon depending on many biotic and abiotic factors. Besides the presence of recalcitrant polymers, the presence of compounds with antimicrobial properties is known to be important to explain wood durability. Based on the advancement in our understanding of fungal detoxification systems, a reverse chemical ecology approach was proposed to explore wood natural durability using fungal glutathione transferases. A set of six glutathione transferases from the white-rot Trametes versicolor were used as targets to test wood extracts from seventeen French Guiana neotropical species. Fluorescent thermal shift assays quantified interactions between fungal glutathione transferases and these extracts. From these data, a model combining this approach and wood density significantly predicts the wood natural durability of the species tested previously using long-term soil bed tests. Overall, our findings confirm that detoxification systems could be used to explore the chemical environment encountered by wood-decaying fungi and also wood natural durability. © 2020 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. |
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Université de Lorraine, INRAE, LERMAB, Nancy, France |
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John Wiley and Sons Ltd |
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17517907 (Issn) |
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EcoFoG @ webmaster @ |
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955 |
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Servigne, P.; Orivel, J.; Azémar, F.; Carpenter, J.; Dejean, A.; Corbara, B. |
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An uneasy alliance: a nesting association between aggressive ants and equally fierce social wasps |
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Journal Article |
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Year |
2020 |
Publication |
Insect Science |
Abbreviated Journal |
Insect Science |
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27 |
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1 |
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122-132 |
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Azteca chartifex ants; interspecific association; mutualism; Polybia rejecta wasps; scent trail erasure |
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Although the Neotropical territorially dominant arboreal ant Azteca chartifex Forel is very aggressive towards any intruder, its populous colonies tolerate the close presence of the fierce polistine wasp Polybia rejecta (F.).
In French Guiana, 83.33% of the 48 P. rejecta nests recorded were found side by side with those of A. chartifex. This nesting association results in mutual protection from predators (i.e., the wasps protected from army ants; the ants protected from birds).
We conducted field studies, laboratory-based behavioral experiments and chemical analyses to elucidate the mechanisms allowing the persistence of this association. Due to differences in the cuticular profiles of the two species, we eliminated the possibility of chemical mimicry.
Also, analyses of the carton nests did not reveal traces of marking on the envelopes. Because ant forager flows were not perturbed by extracts from the wasps' Dufour's and venom glands, we rejected any hypothetical action of repulsive chemicals. Nevertheless, we noted that the wasps 'scraped' the surface of the upper part of their nest envelope using their mandibles, likely removing the ants' scent trails, and an experiment showed that ant foragers were perturbed by the removal of their scent trails. This leads us to use the term 'erasure hypothesis'. Thus, this nesting association persists thanks to a relative tolerance by the ants towards wasp presence and the behavior of the wasps that allows them to 'contain' their associated ants through the elimination of their scent trails, direct attacks, 'wing-buzzing' behavior and ejecting the ants. |
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John Wiley & Sons, Ltd (10.1111) |
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1672-9609 |
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doi: 10.1111/1744-7917.12597 |
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EcoFoG @ webmaster @ |
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885 |
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Talaga, S.; Dejean, A.; Mouza, C.; Dumont, Y.; Leroy, C. |
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Larval interference competition between the native Neotropical mosquito Limatus durhamii and the invasive Aedes aegypti improves the fitness of both species |
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Journal Article |
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2018 |
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Insect Science |
Abbreviated Journal |
Insect Science |
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25 |
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1102-1107 |
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Aedes aegypti; increased fitness; interference competition; Limatus durhamii; phenotypic plasticity; resistance to invasion |
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Abstract Interspecific competition with native species during biological invasions can sometimes limit alien expansion. We aimed to determine the potential ecological effects of Limatus durhamii Theobald 1901, a native Neotropical mosquito (Diptera: Culicidae) species, on the invasive species Aedes (Stegomyia) aegypti (Linnaeus 1762) that breeds in the same artificial water containers. Development time and adult dry mass were measured in 3 rearing conditions: control (a single larva), intraspecific competition (2 conspecific larvae), and interspecific competition (2 heterospecific larvae). Food was provided ad libitum to eliminate exploitative competition. For Ae. aegypti, development time was not affected by interspecific interference competition (nonsignificant differences with the control) and the adult dry mass was significantly higher, meaning that individual fitness likely increased. Yet, because previous studies showed longer development time and lighter adults during competition with other invasive mosquitoes, it is likely that Ae. aegypti can express a different phenotype depending on the competing species. The similar pattern found for Li. durhamii females and the nonsignificant difference with the control for males explain in part why this species can compete with Ae. aegypti. |
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John Wiley & Sons, Ltd (10.1111) |
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1672-9609 |
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EcoFoG @ webmaster @ |
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836 |
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Dejean, A.; Corbara, B.; Céréghino, R.; Leponce, M.; Roux, O.; Rossi, V.; Delabie, J.H.C.; Compin, A. |
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Traits allowing some ant species to nest syntopically with the fire ant Solenopsis saevissima in its native range |
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Journal Article |
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2015 |
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Insect Science |
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Insect Science |
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22 |
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2 |
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289-294 |
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Ant community; Fire ants; Invasive species; Solenopsis saevissima; Species coexistence; Supercoloniality |
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Supercolonies of the red fire ant Solenopsis saevissima (Smith) develop in disturbed environments and likely alter the ant community in the native range of the species. For example, in French Guiana only 8 ant species were repeatedly noted as nesting in close vicinity to its mounds. Here, we verified if a shared set of biological, ecological, and behavioral traits might explain how these 8 species are able to nest in the presence of S. saevissima. We did not find this to be the case. We did find, however, that all of them are able to live in disturbed habitats. It is likely that over the course of evolution each of these species acquired the capacity to live syntopically with S. saevissima through its own set of traits, where colony size (4 species develop large colonies), cuticular compounds which do not trigger aggressiveness (6 species) and submissive behaviors (4 species) complement each other. © 2013 Institute of Zoology, Chinese Academy of Sciences. |
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U.P.A. Laboratório de Mirmecologia, Convênio UESC/CEPLAC, C.P. 7Itabuna, Bahia, Brazil |
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Export Date: 9 April 2015 |
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EcoFoG @ webmaster @ |
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594 |
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Legeay, J.; Husson, C.; Boudier, B.; Louisanna, E.; Baraloto, C.; Schimann, H.; Marcais, B.; Buée, M. |
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Surprising low diversity of the plant pathogen Phytophthora in Amazonian forests |
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Journal Article |
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Year |
2020 |
Publication |
Environmental Microbiology |
Abbreviated Journal |
Environ. Microbiol. |
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Volume |
22 |
Issue |
12 |
Pages |
5019-5032 |
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The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them cause the collar and root-rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in the Neotropical forests where natural enemies could maintain the huge plant diversity via negative density dependence. We characterized the diversity of soil-borne Phytophthora communities in the North French Guiana rainforest and investigated how they are structured by host identity and environmental factors. In this little-explored habitat, 250 soil cores were sampled from 10 plots hosting 10 different plant families across three forest environments (Terra Firme, Seasonally Flooded and White Sand). Phytophthora diversity was studied using a baiting approach and metabarcoding (High-Throughput Sequencing) on environmental DNA extracted from both soil samples and baiting-leaves. These three approaches revealed very similar communities, characterized by an unexpected low diversity of Phytophthora species, with the dominance of two cryptic species close to Phytophthora heveae. As expected, the Phytophthora community composition of the French Guiana rainforest was significantly impacted by the host plant family and environment. However, these plant pathogen communities are very small and are dominated by generalist species, questioning their potential roles as drivers of plant diversity in these Amazonian forests. © 2020 Society for Applied Microbiology and John Wiley & Sons Ltd. |
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International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL 33199, United States |
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Blackwell Publishing Ltd |
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14622912 (Issn) |
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EcoFoG @ webmaster @ |
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940 |
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Vergne, Antoine ; Darbot, Vincent ; Bardot, Corinne ; Enault, François ; Le Jeune, Anne-Hélène ; Carrias, Jean-François ; Corbara, Bruno ; Céréghino, Régis ; Leroy, Celine ; Jeanthon, Christian ; Giraud, Eric ; Mary, Isabelle ; Lehours, Anne-Catherine |
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Assemblages of anoxygenic phototrophic bacteria in tank bromeliads exhibit a host-specific signatureit |
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Journal Article |
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Year |
2021 |
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Journal of Ecology |
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109 |
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7 |
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2550-2565 |
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Anoxygenic phototrophic bacteria (APB) are a very significant metabolic functional group in the phytotelmata of tank-forming Bromeliaceae plants. Considering the close relationships existing between the bromeliad and its tank microbiota, the dominance of APB raises the question of their role in the ecology and evolution of these plants. Here, using pufM gene sequencing for taxonomic profiling, we investigated the structure of APB communities in the tanks of five bromeliad species exhibiting different habitat characteristics (i.e. physicochemical factors associated with the host), and occurring in different localities of French Guiana.
We found that APB assemblages were specific to plant species and were less dependent on location or on bromeliad habitat characteristics. This convergence suggests that the identity of the bromeliad species per se is more important than habitat filtering or dispersal to control specific assembly rules for APB. The pufM OTUs were affiliated with five orders of Alpha- and Beta-proteobacteria (Rhodobacterales, Sphingomonadales, Rhizobiales, Burkholderiales and Rhodospirillales), and we assume that they may be major components of the core microbiota of plant-held waters. Our findings also revealed that up to 79% of the sequences were affiliated with APB clades possessing nitrogen-fixing genes suggesting that this metabolic capability is widespread within the APB community inhabiting tank bromeliads. We hypothesized that bromeliads may benefit nutritionally from associations with free-living APB capable to fix atmospheric nitrogen. Synthesis. Understanding the dominance of APB in tank bromeliads and determining whether a potential interplay exists between these partners is an intriguing aspect of possible mutualistic and coevolving interactions between the two existing forms of chlorophototrophy (i.e. bacteriochlorophyll-based anoxygenic and chlorophyll-based oxygenic phototrophy). In the present study, we found that bromeliad species was the main factor that explained variance in APB community composition. These findings suggest that APB and tank bromeliads may have a close, mutualistic relationship and we hypothesize according to our genomic analyses that APB may promote the bromeliad growth by provisioning essential nutrients like nitrogen. |
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British Ecological Society |
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EcoFoG @ webmaster @ |
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1023 |
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Bonhomme, Camille ; Céréghino, Régis ; Carrias, Jean-François ; Compin, Arthur ; Corbara, Bruno ; Jassey, Vincent E.J. ; Leflaive, Joséphine ; Farjalla, Vinicius F. ; Marino, Nicholas A.C. ; Rota, Thibault ; Srivastava, Diane S. ; Leroy, Celine |
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In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a neotropical ecosystem |
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Journal Article |
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Year |
2021 |
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Journal of Animal Ecology |
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90 |
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9 |
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2015-2026 |
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While future climate scenarios predict declines in precipitations in many regions of the world, little is known of the mechanisms underlying community resilience to prolonged dry seasons, especially in ‘naïve’ Neotropical rainforests. Predictions of community resilience to intensifying drought are complicated by the fact that the underlying mechanisms are mediated by species' tolerance and resistance traits, as well as rescue through dispersal from source patches. We examined the contribution of in situ tolerance-resistance and immigration to community resilience, following drought events that ranged from the ambient norm to IPCC scenarios and extreme events. We used rainshelters above rainwater-filled bromeliads of French Guiana to emulate a gradient of drought intensity (from 1 to 3.6 times the current number of consecutive days without rainfall), and we analysed the post-drought dynamics of the taxonomic and functional community structure of aquatic invertebrates to these treatments when immigration is excluded (by netting bromeliads) or permitted (no nets). Drought intensity negatively affected invertebrate community resistance, but had a positive influence on community recovery during the post-drought phase. After droughts of 1 to 1.4 times the current intensities, the overall invertebrate abundance recovered within invertebrate life cycle durations (up to 2 months). Shifts in taxonomic composition were more important after longer droughts, but overall, community composition showed recovery towards baseline states. The non-random patterns of changes in functional community structure indicated that deterministic processes like environmental filtering of traits drive community re-assembly patterns after a drought event. Community resilience mostly relied on in situ tolerance-resistance traits. A rescue effect of immigration after a drought event was weak and mostly apparent under extreme droughts. Under climate change scenarios of drought intensification in Neotropical regions, community and ecosystem resilience could primarily depend on the persistence of suitable habitats and on the resistance traits of species, while metacommunity dynamics could make a minor contribution to ecosystem recovery. Climate change adaptation should thus aim at identifying and preserving local conditions that foster in situ resistance and the buffering effects of habitat features. |
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British Ecological Society |
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EcoFoG @ webmaster @ |
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1012 |
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Trzcinski, M.K.; Srivastava, D.S.; Corbara, B.; Dezerald, O.; Leroy, C.; Carrias, J.-F.; Dejean, A.; Céréghino, R.; Rudolf, V. |
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The effects of food web structure on ecosystem function exceeds those of precipitation |
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Journal Article |
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Year |
2016 |
Publication |
Journal of Animal Ecology |
Abbreviated Journal |
Journal of Animal Ecology |
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Volume |
85 |
Issue |
5 |
Pages |
1147-1160 |
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bromeliad; climate change; community interactions; drought; ecosystem function; French Guiana; invertebrates; micro-organisms; phytotelmata; precipitation |
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Abstract |
Ecosystems are being stressed by climate change, but few studies have tested food web responses to changes in precipitation patterns and the consequences to ecosystem function. Fewer still have considered whether results from one geographic region can be applied to other regions, given the degree of community change over large biogeographic gradients. We assembled, in one field site, three types of macroinvertebrate communities within water-filled bromeliads. Two represented food webs containing both a fast filter feeder–microbial and slow detritivore energy channels found in Costa Rica and Puerto Rico, and one represented the structurally simpler food webs in French Guiana, which only contained the fast filter feeder–microbial channel. We manipulated the amount and distribution of rain entering bromeliads and examined how food web structure mediated ecosystem responses to changes in the quantity and temporal distribution of precipitation. Food web structure affected the survival of functional groups in general and ecosystem functions such as decomposition and the production of fine particulate organic matter. Ecosystem processes were more affected by decreased precipitation than were the abundance of micro-organisms and metazoans. In our experiments, the sensitivity of the ecosystem to precipitation change was primarily revealed in the food web dominated by the single filter feeder–microbial channel because other top-down and bottom-up processes were weak or absent. Our results show stronger effects of food web structure than precipitation change per se on the functioning of bromeliad ecosystems. Consequently, we predict that ecosystem function in bromeliads throughout the Americas will be more sensitive to changes in the distribution of species, rather than to the direct effects caused by changes in precipitation. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society |
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Boulevard de la Lironde, IRD, botAnique et bioinforMatique de l'Architecture des Plantes (UMR-IRD 123), TA A-51/PS2, Montpellier Cedex 5, France |
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Export Date: 1 September 2016 |
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EcoFoG @ webmaster @ |
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685 |
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